Contacts of the helix formed by residues 581 - 601 (chain A) in PDB entry 1NHX
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with SER 581 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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440A GLY* 5.3 1.7 + - - -
518A ARG* 5.8 2.2 - - - +
579A SER* 4.0 3.8 + - - -
580A ILE* 1.3 73.7 - - - +
582A LYS* 1.3 64.6 + - - +
583A GLU* 3.4 9.7 + - - +
584A PHE* 3.0 27.0 + - - +
585A TRP* 3.0 30.7 + - - +
622A MET* 4.4 1.6 - - - -
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Residues in contact with LYS 582 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
580A ILE 3.9 3.0 + - - -
581A SER* 1.3 70.8 - - - +
583A GLU* 1.3 54.2 + - - +
586A ASP* 2.8 56.2 + - - +
619A ILE* 3.8 18.5 - - + +
620A SER* 3.4 24.5 + - - +
622A MET* 3.7 51.0 - - + +
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Residues in contact with GLU 583 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
581A SER* 3.7 7.0 - - - +
582A LYS* 1.3 81.3 - - - +
584A PHE* 1.3 64.5 + - - +
586A ASP* 3.6 8.4 + - - +
587A LYS* 3.4 38.4 + - + +
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Residues in contact with PHE 584 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
437A ARG* 3.3 26.9 - - - -
439A ALA* 3.4 33.7 - - + -
440A GLY* 3.7 23.6 - - - -
441A VAL* 4.1 7.0 - - + -
581A SER* 3.0 24.0 + - - +
583A GLU* 1.3 76.6 - - - +
585A TRP* 1.3 80.4 + + + +
587A LYS* 3.3 27.3 + - - +
588A GLU* 2.9 43.2 + - + +
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Residues in contact with TRP 585 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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440A GLY 3.0 20.5 + - - -
441A VAL* 4.0 26.9 - - + -
442A PRO* 4.4 0.2 - - + -
445A TYR* 4.5 14.8 - + - -
555A ILE* 3.7 44.9 - - + -
580A ILE* 3.7 24.0 - - + +
581A SER 3.0 29.9 + - - +
582A LYS* 4.2 2.0 - - - +
584A PHE* 1.3 82.8 - + - +
586A ASP* 1.3 65.8 + - - +
587A LYS 3.3 0.2 - - - -
588A GLU* 3.6 32.2 - - + +
589A VAL* 3.0 27.0 + - - +
592A ILE* 5.0 4.0 - - + -
615A LEU* 4.8 13.2 - - + -
619A ILE* 3.4 28.0 - - + +
622A MET* 5.5 0.9 - - - -
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Residues in contact with ASP 586 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
582A LYS* 2.8 45.5 + - - +
583A GLU* 3.6 8.6 - - - +
585A TRP* 1.3 72.1 - - - +
587A LYS* 1.3 61.8 + - + +
589A VAL* 3.5 8.7 - - - +
590A GLU* 3.2 25.3 + - - +
619A ILE* 3.4 20.0 - - - +
620A SER* 5.2 1.9 + - - -
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Residues in contact with LYS 587 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
583A GLU* 3.4 36.7 + - + +
584A PHE* 3.3 28.2 + - - +
586A ASP* 1.3 77.2 - - + +
588A GLU* 1.3 67.5 + - - +
590A GLU* 3.4 13.6 + - - +
591A ASP* 2.9 25.3 + - - +
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Residues in contact with GLU 588 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
437A ARG* 2.9 42.9 + - - -
459A ALA 5.0 1.2 - - - +
461A ARG* 3.1 28.4 + - - +
584A PHE* 2.9 28.9 + - + +
585A TRP* 3.3 41.0 + - + +
587A LYS* 1.3 76.6 - - - +
589A VAL* 1.3 58.7 + - - +
591A ASP* 3.2 6.3 + - - +
592A ILE* 2.8 43.6 + - + +
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Residues in contact with VAL 589 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
455A PHE* 5.2 1.1 - - + -
585A TRP 3.0 19.2 + - - +
586A ASP* 3.5 11.2 - - - +
588A GLU* 1.3 77.7 - - - +
590A GLU* 1.3 55.2 + - - +
592A ILE* 4.2 9.9 - - + -
593A GLU* 2.8 34.4 + - - +
612A ILE* 3.9 26.7 - - + +
615A LEU* 3.9 26.2 - - + -
616A LYS* 3.7 29.2 - - + -
619A ILE* 3.9 17.0 - - + -
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Residues in contact with GLU 590 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
586A ASP 3.2 19.3 + - - +
587A LYS* 3.7 12.8 - - - +
589A VAL* 1.3 75.9 - - - +
591A ASP* 1.3 64.3 + - - +
593A GLU* 4.0 9.1 - - - +
594A LYS* 3.1 27.6 + - + +
616A LYS* 5.9 0.9 - - - -
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Residues in contact with ASP 591 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
461A ARG* 3.1 35.3 + - - +
477A HIS* 2.6 34.1 + - - -
587A LYS 2.9 18.4 + - - +
588A GLU 3.5 3.8 - - - +
590A GLU* 1.3 77.2 - - - +
592A ILE* 1.3 61.8 + - - +
594A LYS* 3.4 7.2 + - - +
595A TYR* 3.1 22.0 + - - +
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Residues in contact with ILE 592 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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455A PHE* 3.7 28.5 - - + -
459A ALA* 3.7 44.2 - - + +
477A HIS* 4.3 10.5 - - + -
585A TRP* 5.0 3.8 - - + -
588A GLU* 2.8 49.9 + - + +
589A VAL* 3.7 9.2 - - + +
591A ASP* 1.3 74.0 - - - +
593A GLU* 1.3 64.4 + - - +
595A TYR* 3.3 1.9 + - - +
596A LEU* 3.0 36.5 + - + +
612A ILE* 4.9 0.7 - - + -
615A LEU* 4.9 6.1 - - + -
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Residues in contact with GLU 593 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
589A VAL 2.8 20.4 + - - +
590A GLU* 4.0 8.6 - - - +
592A ILE* 1.3 73.5 - - - +
594A LYS* 1.3 64.4 + - - +
596A LEU* 3.9 0.2 - - - -
597A VAL* 2.9 43.6 + - + +
612A ILE* 3.7 32.7 - - + +
616A LYS* 2.6 37.9 + - + +
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Residues in contact with LYS 594 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108A THR* 5.0 8.4 + - - +
590A GLU* 3.1 21.4 + - + +
591A ASP* 3.8 7.2 - - - +
593A GLU* 1.3 77.2 - - - +
595A TYR* 1.3 60.8 + - - +
597A VAL* 5.0 2.0 - - - -
598A ASP* 2.9 52.5 + - - +
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Residues in contact with TYR 595 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112A GLN* 3.8 23.0 + - - +
113A LEU* 3.6 23.1 - - + +
458A ALA 5.0 1.8 - - - -
477A HIS* 3.3 61.2 - + + +
479A PRO* 3.9 14.0 - - + +
483A ARG* 3.8 16.1 - - - -
490A PHE* 5.5 0.2 - + - -
591A ASP* 3.1 17.7 + - - +
592A ILE 3.8 1.8 - - - +
594A LYS* 1.3 79.1 - - + +
596A LEU* 1.3 76.8 + - + +
598A ASP* 4.5 2.7 - - - -
599A GLN* 2.8 54.9 + - + +
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Residues in contact with LEU 596 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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455A PHE* 4.4 3.6 - - + -
458A ALA* 3.8 32.3 - - + +
459A ALA* 5.6 0.2 - - - -
490A PHE* 4.1 23.1 - - + -
494A LEU* 5.1 0.2 - - + -
592A ILE* 3.0 37.8 + - + +
593A GLU 4.2 1.6 - - - +
595A TYR* 1.3 85.6 - - + +
597A VAL* 1.3 61.9 + - - +
600A VAL* 2.9 40.6 + - + +
601A ASN 3.6 0.5 + - - -
604A LEU* 4.0 15.3 - - + +
608A ILE* 4.1 16.6 - - + -
612A ILE* 4.0 20.2 - - + -
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Residues in contact with VAL 597 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107A LYS* 3.5 27.7 - - + -
593A GLU* 2.9 36.7 + - + +
594A LYS* 4.4 1.8 - - - +
596A LEU* 1.3 75.0 - - - +
598A ASP* 1.3 62.1 + - - +
601A ASN* 3.1 24.1 + - - +
604A LEU* 4.1 19.1 - - + -
609A GLU* 6.1 1.6 - - + -
612A ILE* 4.8 5.4 - - + -
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Residues in contact with ASP 598 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106A PRO* 3.2 2.1 - - - +
107A LYS* 2.7 40.4 + - - +
108A THR* 2.6 47.1 + - - +
594A LYS* 2.9 37.6 + - - +
595A TYR* 3.8 3.8 - - - +
597A VAL* 1.3 80.5 - - - +
599A GLN* 1.3 83.0 + - - +
601A ASN* 3.9 1.6 - - - +
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Residues in contact with GLN 599 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104A PRO* 3.4 19.1 - - - +
106A PRO* 4.0 18.7 - - - +
108A THR 4.3 1.6 + - - -
110A LEU 3.6 19.0 + - - -
111A SER* 3.5 6.4 + - - -
112A GLN* 2.7 39.5 + - - +
113A LEU* 3.4 26.6 - - + +
595A TYR* 2.8 49.3 + - + +
598A ASP* 1.3 96.2 + - + +
600A VAL* 1.3 60.2 + - + +
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Residues in contact with VAL 600 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104A PRO* 3.6 10.5 - - + +
113A LEU* 4.2 2.2 - - + -
490A PHE* 3.7 28.9 - - + -
491A GLY* 3.5 30.5 - - - +
494A LEU* 4.6 1.8 - - + -
596A LEU* 2.9 24.9 + - + +
599A GLN* 1.3 78.8 - - + +
601A ASN* 1.3 63.3 + - - +
602A ALA 3.2 0.9 + - - -
603A ASP* 2.9 26.8 + - + +
604A LEU* 3.4 39.3 - - + +
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Residues in contact with ASN 601 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105A ILE* 2.9 31.4 + - - +
106A PRO 3.6 3.6 + - - -
107A LYS* 2.7 51.5 + - - +
596A LEU 3.6 1.2 + - - -
597A VAL* 3.1 20.9 + - - +
598A ASP 3.9 6.3 - - - +
600A VAL* 1.3 76.9 - - - +
602A ALA* 1.3 73.2 + - - +
603A ASP 3.1 1.2 + - - -
604A LEU* 3.3 16.5 + - - +
609A GLU* 5.6 1.2 - - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il